Breaks-independent recognition of homology in chromosomes is one of the remaining mysteries in the field of genome structure and function. It has been shown to be important in various organisms, in both somatic and meiotic cells. Such essential processes as regulation of gene expression, meiosis, X-chromosome dosage compensation and genomic surveillance for rearrangements, seem to rely on this phenomenon. Malfunction of meiosis is the leading cause of miscarriages and mental retardation in humans;malfunction of gene expression, as well as failure to maintain genomic stability, lead to cancer. Therefore, information about this important process is crucial for our understanding and possible control of these maladies. Yet its molecular mechanism is not known. Here, I propose to study breaks-independent pairing of homologous chromosomes in the budding yeast, using two complementary approaches. First, I will perform genome-wide high-resolution scan for pairing frequencies. Identification of regions with greater and lesser pairing activity will help to identify relevant determinants;additionally, identification of especially strong "hot spots" will facilitate direct investigation of the molecular mechanism of this process. Second, I will analyze a known pairing-active locus and assess whether pairing involves direct DNA/DNA recognition, or certain candidate genomic elements such as structure-prone DNA sequences and protein binding sites. For both approaches, I plan to employ the Chromosome Conformation Capture (3C) technique, recently developed in Dr. Kleckner's laboratory for studying three-dimensional conformation of chromosomes within nuclei. For the first aim, I have formulated a new version of this methodology as specifically required for this purpose. The proposed adaptation will expand the range of problems approachable by 3C to include not only interhomolog contacts but also inter-sister contacts, with many potential general applications. In the long run, my goal is to explain how homologous chromosomes recognize each other in the absence of breaks and to define the role that this recognition plays in fundamental genomic functions. This proposal focuses on studying interactions between homologous chromosomes, which are involved in meiosis, regulation of gene expression and maintenance of genomic stability. Malfunction of meiosis is the leading cause of miscarriages and mental retardation in humans;malfunction of gene expression, as well as failure to maintain genomic stability, lead to cancer. Therefore, information about this important process is crucial for our understanding and possible control of these maladies.